I am using SuperSpeed Explorer Kit to develop code communicate with SPI slave device. The issue I have is the debug port, I only can see the debug output in USBBulkSourceSinkLED project, none of other project such as UsbSpiDmaMode debug port works.

I have been tried many sample project from SDK, none of them work too. Since USBBulkSourceSinkLED works, I am assuming the hardware is fine.

I checked the code, it's pretty much the same code to init and DebugPrint() function. Not very sure what's going on.

That will move your UART down to pins GPIO[46] - GPIO[49] and enable SPI on the old UART pins of GPIO[53] -GPIO[57]. This means that the SPI connection will be wired to the UART debug chip, and the new UART Debug output will be wired to nothing. So you wont get anything unless you connect another USB to UART chip like an FTDI Friend to the new UART output.